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Bchem 393 > Genetic Code And Protien Synthesis > Flashcards

Genetic Code And Protien Synthesis Flashcards

1
Q

What is the genetic code

Which way is it read

A

3 nucleotide sequences in the mRNA that form amino acids

Universal

These are read from 5’ to 3’ in the mRNA

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2
Q

What is degeneracy in the genetic code

What are synonymous codons

A

More than one codon (three letter sequence) codes a specific AA

They are the codons that are all different but code for the same AA

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3
Q

What is codon bias

A

When an organism prefers one specific type of codon to code and AA

rather than another codon that codes the exact same thing

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4
Q

What are the start codons

Stop codons

A

AUG

UAA, UAG, UGA

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5
Q

What type of molecules are tRNA

A

Adaptor molecules

(Link multiple protiens together)

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6
Q

What is the structure of tRNA

A

Small

L shaped

5’ end is phosphorylated and has and anticodon loop (where it base pairs with rna codon)

3’ end has a CCA component where the amino acid is attached

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7
Q

tRNA’s have modified bases that base pair with the mRNA

what is one and how is it formed

A

Inosine

It’s made when adenosine (adenine base and a sugar) is deaminated

If just adenine deaminated it’s hypoxanthine

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8
Q

Why is it important for tRNA to have a modified base like inosine

What bases can inosine pair with

A

Because it is able to do wobble base pairing where one tRNA codon is able to recognize more than one codon in the mRNA

Inosine is in the third position of the anticodon and can pair with C U AND A

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9
Q

How does inspire helping in wobble base pairing show degeneracy in the genetic code

A

Since the specific TRNA anticodon with Inosine can bind to many diff mRNA codons, the same amino acid is made for those many codons

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10
Q

What is tRNA charging

A

It involves the 3’ CCA arm

amino acids are added to the tRNA CCA arm

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11
Q

Why does the tRNA have to be activated first before starting translation and making proteins

A

Because forming peptide bonds between free amino acids is thermodynamically unfavourable

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12
Q

What is the activated intermediate of tRNA

What is it called

A

The activated intermediated is an amino acid ester

It’s called aminoacyl tRNA

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13
Q

How is the amino acids to be added to the 3’ end of the tRNA activated

A

By the adenylation (adding adenines) of the amino acids

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14
Q

After the amino acid for tRNA charging is activated what does it turn into and where does it go

A

It turns into aminoacyl-AMP and is transferred to the tRNA 3’ end

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15
Q

What catalyzes the adenylation of the amino acid and the transfer of it to the tRNA

A

Aminoacyl tRNA synthetase

This is what ultimately makes the charged tRNA

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16
Q

What is the first activation by adenylation step of tRNA charging

What makes the amino acid actually get activated

A

This is where the carboxy group of the amino acid attacks the alpha phosphate of the atp (adenylate)

This releases PPi and makes aminoacyl-AMP

The amino acid is now activated by the phosphoester bond between the AA and the phosphate of the amp

17
Q

What is the 2nd transfer to tRNA step of tRNA charging

What charges the tRNA

A

The 3’ oh of the Adenine of the 3’ CCA of the tRNA attacks the caboxy group of the amino acid in the amino acyl amp

This releases amp and forms aminoacyl- tRNA

The ester linkage of the 3’ OH of the adenosine from CCA and the amino acid charges the tRNA

18
Q

What does the aminoacyl tRNA synthetase do in tRNA charging

A

It bind to the tRNA and AA and ATP

This allows all the reactions to happen to make the charge tRNA

19
Q

Because each aminoacyl tRNA synthetase is specific to only one amino acid that it adds to the tRNA

What is an example of something that could get mixed up

A

Example. If threonyl-tRNA synthetase want threonine (oh side group with methyl)

But valine (ch3 side group) and serine (oh but no methyl) are similar to threonine

Need to find a way to get only thr and not Val or ser

20
Q

How does threonyl - tRNA synthetase make sure valine does not get mixed up with threonine

A

It all depends on the zinc in the active site of the enzyme.

The Val side chain methyl prevents interaction with the enzymes active zinc because it’s not an oh

So it doesn’t get attached to the enzyme

21
Q

How does threonyl - tRNA synthetase make sure serine does not get mixed up with threonine

A

Since the serine also has an OH, it can attach to the activation site zinc of the enzyme.

This means it does get attached to the tRNA

But the enzyme has an editing site where the serine can’t fit into because of it doesn’t have the extra methyl group that the does

So it doesn’t stay in the tRNA

22
Q

What is the ribosome made up of

A

ribosomal rna and protiens

It has a 30s subunit and 50s subunit to make up the 70s ribosome

It has the E P A three binding sites for tRNA in the ribosome

23
Q

What does E P A stand for

A

Exit

Peptidyl

Amino acyl

24
Q

What is the direction of translation?

A

On the 5’-3’ mRNA the ribosome moves in a 5’-3’direction on the mRNA

25
Q

How is translation initiated in bacteria by forming the 30s initiation complex

A

First the 30s unit of the ribosome forms a complex with IF1 and 3 (initiation factors)

This makes it so the the 30s doesn’t prematurely bind to the 50s subunit

Then the IF2 binds to GTP and then to fMET trna (the thing that adds fMET)

This if2 GTP F met tRNA binds to the mRNA AUG and the 30s subunit to make the 30s initiation complex

26
Q

When the 30s initiation complex is made, what happens

A

The 70s initiation complex is formed by IF1 and 3 leaving the 30s subunit

This causes the 50s subunit to come to the 30s subunit

Once the 50s subunit arrives, the GTP on IF2 is hydrolyzed and IF2 leaves

This forms the 70s initiation complex where the fMET tRNA is at the p site

27
Q

How does elongation occurs once the ribosome has been created on the start codon

A

EF-Tu-GTP binds to aminoacyl-tRNAs and moves them to the A site of the ribosome

If the base pairing is right, the EF-Tu hydrolyzes GTP to gdp and releases the aminoacyl tRNA to the A site

28
Q

What does Ef-Tu-GTP protect

A

The ester linkage in the aminoacyl tRNA

29
Q

Once both the A site and the P site are occupied by aminoacyl tRNAs what happens

A

Need to make a peptide bond between the two AA

The fMET carboxy group on the P site initiatior tRNA gets attacked by the amino group of the amino acid on the A site tRNA

This means the new peptide bonds are formed on the tRNA in the A site

30
Q

Once a peptide bond is forms and the two amino acids are on the A site MRNA, what happens

Where does each thing go

A

Translocation occurs

The mRNA along with tRNA attached to it shifts over to the 5’ end by three nucleotides

This makes it so that the next three nucleotides (codon) are in the A site.

The tRNA with the growing chain moves to the P site and the fMET tRNA move to the e site

31
Q

During translocation, how does the MRNA actually move to the left by three nucleotides

A

EF-G near the A site bind and hydrolyzes GTP and pushes the mRNA and tRNA to the left by one codon

32
Q

How is termination done

A

RF1 or 2 protiens recognize the stop codons and bind at the A SITE stop codon

Once bound, they hydrolyze the last ester linkage between the peptide and the TRNA in the p site

This release the peptide

33
Q

After the peptide is released in termination, what can happens to it

A

It can be post translationally modified

34
Q

After the peptide is gone due to termination how does RF1 or RF2 leave

How is the ribosome disassembled

A

Rf3-GTP hydrolyzes GTP and indirectly makes RF1 or RF2 leave the mRNA

EF-G hydrolyzes GTP and triggers the ribosome to disassemble

35
Q

What are the enzymes that hydrolyze atp of GTP in

TRNA charging

Initiation

Elongation

Termination

A

Trna charging: aminoacyltrnasynthestase (ATP)

Initiation: IF2 (GTP)

Elongation: EF-Tu (GTP), EF-G (GTP)

Termination: RF3 (GTP), EF-G (GTP)

36
Q

What are the most commonly modified amino acid side chains in post translation modification

How can they be modified

A

Ones with OH, amino or Thiol functional groups

Ex. Ser/thr with OH side chain can be phosphorylated or glycosylated

37
Q

What is the effect of postranslational modification?

A

It influences the chemical properties of the protien

Changes the net charge

Changes the confirmation

Changing the binding/function

38
Q

Is postranslational modification reversible?

Is it specific

A

Yes

Yes a specific enzyme catalyzes each modification

39
Q

Which protien is commonly changed by lipidation

Phosphorylation

Glycosylation

A

Things with Thiol groups like cysteine

Things with oh like serine or threonine

Thins with nh2 like aspargine

Bchem 393 (31 decks)

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